From 0a8fdbf4084c064c6839e6283781ede09983e742 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 13 Jun 2024 12:02:36 -0500
Subject: Clean up landing page

Leave only data upload type selection on landing page.
---
 qc_app/entry.py                      | 12 +++--
 qc_app/static/js/select_platform.js  |  2 +-
 qc_app/templates/index.html          | 80 ++-------------------------------
 qc_app/templates/select_species.html | 87 ++++++++++++++++++++++++++++++++++++
 4 files changed, 99 insertions(+), 82 deletions(-)
 create mode 100644 qc_app/templates/select_species.html

diff --git a/qc_app/entry.py b/qc_app/entry.py
index 94bbd53..d23a45a 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -84,20 +84,24 @@ def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
 
     return zfile_errors
 
-@entrybp.route("/", methods=["GET", "POST"])
+@entrybp.route("/", methods=["GET"])
+def index():
+    """Load the landing page"""
+    return render_template("index.html")
+
+@entrybp.route("/upload", methods=["GET", "POST"])
 def upload_file():
     """Enables uploading the files"""
     if request.method == "GET":
         return render_template(
-            "index.html", species=with_db_connection(species))
+            "select_species.html", species=with_db_connection(species))
 
     upload_dir = app.config["UPLOAD_FOLDER"]
     request_errors = errors(request)
     if request_errors:
         for error in request_errors:
             flash(error, "alert-error error-expr-data")
-        return render_template(
-            "index.html", species=with_db_connection(species)), 400
+        return redirect(url_for("entry.upload_file"))
 
     filename = secure_filename(request.files["qc_text_file"].filename)
     if not os.path.exists(upload_dir):
diff --git a/qc_app/static/js/select_platform.js b/qc_app/static/js/select_platform.js
index 456cfcf..4fdd865 100644
--- a/qc_app/static/js/select_platform.js
+++ b/qc_app/static/js/select_platform.js
@@ -12,7 +12,7 @@ function radio_column(chip) {
 function setup_genechips(genechip_data) {
     columns = ["GeneChipId", "GeneChipName"]
     submit_button = document.querySelector(
-	"#select-platform-form input[type='submit']");
+	"#select-platform-form button[type='submit']");
     elt = document.getElementById(
 	"genechips-table").getElementsByTagName("tbody")[0];
     remove_children(elt);
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 0d301f5..997c1e5 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -60,59 +60,9 @@
     </ol>
   </div>
 
-  <form action="{{url_for('entry.upload_file')}}"
-        method="POST"
-        enctype="multipart/form-data"
-        id="frm-upload-expression-data">
-    <legend class="heading">upload expression data</legend>
-    {{flash_messages("error-expr-data")}}
-
-    <div class="form-group">
-      <label for="select_species01" class="form-label">Species</label>
-      <select id="select_species01"
-	      name="speciesid"
-	      required="required"
-              class="form-control">
-        <option value="">Select species</option>
-        {%for aspecies in species%}
-        <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
-        {%endfor%}
-      </select>
-    </div>
-
-    <div class="form-group">
-      <legend class="heading">file type</legend>
-
-      <div class="form-check">
-        <input type="radio" name="filetype" value="average" id="filetype_average"
-	       required="required" class="form-check-input" />
-        <label for="filetype_average" class="form-check-label">average</label>
-      </div>
-
-      <div class="form-check">
-        <input type="radio" name="filetype" value="standard-error"
-	       id="filetype_standard_error" required="required"
-	       class="form-check-input" />
-        <label for="filetype_standard_error" class="form-check-label">
-          standard error
-        </label>
-      </div>
-    </div>
-
-    <div class="form-group">
-      <span id="no-file-error" class="alert-danger" style="display: none;">
-        No file selected
-      </span>
-      <label for="file_upload" class="form-label">select file</label>
-      <input type="file" name="qc_text_file" id="file_upload"
-	     accept="text/plain, text/tab-separated-values, application/zip"
-	     class="form-control"/>
-    </div>
-
-    <button type="submit" class="btn btn-primary" />upload file</button>
-</form>
-
-{{upload_progress_indicator()}}
+  <a href={{url_for("entry.upload_file")}}
+     title="Upload your expression data"
+     class="btn btn-primary">upload Samples/Cases</a>
 </div>
 
 <div class="row">
@@ -131,27 +81,3 @@
 </div>
 
 {%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript" src="static/js/upload_progress.js"></script>
-<script type="text/javascript">
-  function setup_formdata(form) {
-      var formdata = new FormData();
-      formdata.append(
-	  "speciesid",
-	  form.querySelector("#select_species01").value)
-      formdata.append(
-	  "qc_text_file",
-	  form.querySelector("input[type='file']").files[0]);
-      formdata.append(
-	  "filetype",
-	  selected_filetype(
-	      Array.from(form.querySelectorAll("input[type='radio']"))));
-      return formdata;
-  }
-
-  setup_upload_handlers(
-      "frm-upload-expression-data", make_data_uploader(setup_formdata));
-</script>
-{%endblock%}
diff --git a/qc_app/templates/select_species.html b/qc_app/templates/select_species.html
new file mode 100644
index 0000000..30f99b4
--- /dev/null
+++ b/qc_app/templates/select_species.html
@@ -0,0 +1,87 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+{%from "upload_progress_indicator.html" import upload_progress_indicator%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+<div class="row">
+  <form action="{{url_for('entry.upload_file')}}"
+        method="POST"
+        enctype="multipart/form-data"
+        id="frm-upload-expression-data">
+    <legend class="heading">upload expression data</legend>
+    {{flash_messages("error-expr-data")}}
+
+    <div class="form-group">
+      <label for="select_species01" class="form-label">Species</label>
+      <select id="select_species01"
+	      name="speciesid"
+	      required="required"
+              class="form-control">
+        <option value="">Select species</option>
+        {%for aspecies in species%}
+        <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
+        {%endfor%}
+      </select>
+    </div>
+
+    <div class="form-group">
+      <legend class="heading">file type</legend>
+
+      <div class="form-check">
+        <input type="radio" name="filetype" value="average" id="filetype_average"
+	       required="required" class="form-check-input" />
+        <label for="filetype_average" class="form-check-label">average</label>
+      </div>
+
+      <div class="form-check">
+        <input type="radio" name="filetype" value="standard-error"
+	       id="filetype_standard_error" required="required"
+	       class="form-check-input" />
+        <label for="filetype_standard_error" class="form-check-label">
+          standard error
+        </label>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <span id="no-file-error" class="alert-danger" style="display: none;">
+        No file selected
+      </span>
+      <label for="file_upload" class="form-label">select file</label>
+      <input type="file" name="qc_text_file" id="file_upload"
+	     accept="text/plain, text/tab-separated-values, application/zip"
+	     class="form-control"/>
+    </div>
+
+    <button type="submit" class="btn btn-primary">upload file</button>
+  </form>
+
+  {{upload_progress_indicator()}}
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="static/js/upload_progress.js"></script>
+<script type="text/javascript">
+  function setup_formdata(form) {
+      var formdata = new FormData();
+      formdata.append(
+	  "speciesid",
+	  form.querySelector("#select_species01").value)
+      formdata.append(
+	  "qc_text_file",
+	  form.querySelector("input[type='file']").files[0]);
+      formdata.append(
+	  "filetype",
+	  selected_filetype(
+	      Array.from(form.querySelectorAll("input[type='radio']"))));
+      return formdata;
+  }
+
+  setup_upload_handlers(
+      "frm-upload-expression-data", make_data_uploader(setup_formdata));
+</script>
+{%endblock%}
-- 
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